Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.
Bottom Line: Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA.Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension.Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.
Affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.Show MeSH
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Mentions: In order to investigate the origin of the different twist-stretch couplings in DNA and RNA, we examine the correlation of other helical variables with respect to helical twist. For the base pair axis parameters no or only very modest correlations of y-disp and Tip with respect to changes in twist were observed for both dsRNA and dsDNA (Figure 4). However, in both cases significant coupled changes of x-disp and base pair inclination with respect to the helical axis were found (Figure 4). The x-disp is negative at low twist angles and the positive x-disp-twist correlation found for both RNA and DNA moves the base pairs on average close to the helical axis upon overwinding (increased twist). Hence, the width of the duplexes shrinks with increasing twist and the effect is more drastic for DNA than RNA (Figure 4). A striking difference between the two duplexes is the coupling of inclination and twist, which is of opposite sign for RNA (positive) and DNA (negative) (Figure 4). The increased inclination of RNA base pairs with increasing twist results in a reduced projection of the distance vector between two neighboring base pairs (proportional to local rise) onto the helical (z-) axis and consequently reduces the extension of the duplex along the helical axis (see also interpretation in the next paragraphs). It also results in a closing of the major groove (Figure 5), which for RNA is sterically more easily possible compared to the minor groove (the minor groove width is nearly independent of twist, Figure 5) making the RNA more compact in all directions.
Affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.